A combination of accurate mass measurement and tandem mass spectrometry (both product ion and precursor ion scans) have been used to characterize the major fragment ions observed in the ESI mass spectrum of kynurenine. Kynurenine is a metabolite of tryptophan found in the human lens and is thought to play a role in protecting the retina from UV-induced damage. Three major fragmentation pathways were evident, following initial elimination either of ammonia, H2O and CO or the imine form of glycine. The latter is proposed to occur via the formation of an ion-molecule complex. In the case of loss of H2O and CO from deaminated kynurenine, there is evidence for an acylium ion intermediate, which is not observed for the loss of H2O and CO directly from protonated kynurenine. Product ion scans of deuterated kynurenine enabled the elucidation of structural rearrangements that were not evident in the spectra of the native compound. Since UV filter compounds can often only be isolated in small quantities from the lens, this study forms the basis for the characterization of novel UV filter compounds using mass spectrometry. The approach presented here may also be useful for the characterization of related classes of small molecules.